The 21-year civil war between north and south Sudan officially ended in 2005 but tensions remain between Khartoum and South Sudan, which seceded from the rest of Sudan in July 2011.
Despite a lengthy peace process, negotiations between the two sides have so far failed to resolve some key issues.
Both Khartoum and South Sudan are heavily dependent on oil revenues, and the division of oil wealth is still under discussion. Three-quarters of oil is in South Sudan, but all the infrastructure to export it (pipelines, refineries and Red Sea port) is in the north. Khartoum has lost a lot of revenue from oil since the split.
In January 2012, the dispute over oil reached a crisis point. South Sudan shut down its oil production in protest after Khartoum started to seize some southern crude to compensate for what it called unpaid transit fees.
The demarcation of the 2,000 kilometre north-south border is another contentious issue.
In 2011, both sides agreed to form a demilitarized buffer zone, to be monitored by joint border security teams with the support of international peacekeepers. But this has been difficult to implement because of ongoing disagreement about the location of the border in several key areas, and insecurity in the border regions.
Sudan and South Sudan regularly trade accusations of supporting insurgencies on each other's territory.
Three oil-rich border states, together called the Three Areas, are potential flashpoints between the two countries and there has been a build-up of forces and arms in all three states.
For more on the north-south civil war, see Thomson Reuters Foundation's South Sudan briefing.
Oil-rich Abyei, Southern Kordofan and Blue Nile states lie along the border between Sudan and South Sudan, and are home to many people who fought alongside southern rebels during the civil war.
Major clashes in all three states between pro-Khartoum and pro-Juba forces have forced hundreds of thousands to flee their homes.
Abyei is claimed by both countries, while Southern Kordofan and Blue Nile lie in Sudan.
The status of the oil-rich Abyei state is unresolved. A referendum over whether the state will join the north or the south was promised under the 2005 peace deal, and was meant to have taken place in January 2011. But South Sudan and Sudan cannot agree the terms of the vote.
The state has seen several outbreaks of fighting between north and south troops since 2005, and the Geneva-based research group Small Arms Survey reported a gradual build-up of troops in the area.
In May 2008 clashes displaced tens of thousands and re-ignited fears of a new civil war between north and south Sudan. After that, joint north-south forces began operating in the region. And in July 2009, both sides said they accepted a ruling by an independent arbitration court in The Hague over Abyei's borders, placing the major Heglig and Bamboo oil fields in the north's Southern Kordofan state and leaving huge tracts of fertile land inside Abyei.
But 2011 saw worsening violence with a series of clashes between Khartoum-backed militias and south-linked groups and a build-up of government troops from both sides, culminating in a full-scale military takeover by Sudanese forces in May. About a third of civilian structures were razed in Abyei town, according to the Satellite Sentinel Project. Around 110,000 people – mostly Ngok Dinka residents - fled the area.
The following month, both north and south agreed to demilitarize Abyei and allow U.N. troops to monitor the peace. They also agreed to the appointment of a new Abyei administration, which had been unilaterally dissolved by South Sudan in May.
The United Nations established a new peacekeeping force, called the United Nations Interim Security Force for Abyei (UNISFA), with a mandate of 4,000 Ethiopian troops.
Just under half that number had been deployed by January 2012, and the United Nations said Khartoum was restricting their movement. A spokesman for the government denied the charge.
In January 2012, Khartoum forces were still in control of Abyei.
Tensions are also high between the pro-Khartoum Missiriya tribe and the Ngok Dinka who want Abyei to join South Sudan. Abyei's fertile land is used all year round by the Ngok Dinka, who have ethnic ties to the south, and for part of the year by the northern Arab Missiriya nomads.
The Ngok Dinka are demanding that voting in the referendum be limited to those who have lived in the area uninterrupted for a long period. This would exclude the Missiriya, who migrate with their cattle seasonally. The Missiriya have threatened war if they are not given ballots.
The Missiriya fear they will lose grazing rights and their livelihoods if an international border runs through their grazing land, even though these rights are enshrined in the 2005 peace deal.
The Khartoum government armed many Missiriya to fight as proxy militias in the civil war.
Southern Kordofan lies in north Sudan, along the disputed border with South Sudan. It is home to the most productive oil fields under Khartoum's control.
Many in the state sided with the southern rebels during the civil war, and feel betrayed by the 2005 peace deal which put the state under Khartoum's control.
In the 1980s local discontent at political marginalisation drove many Nuba to sympathise with the southern rebels.
The Nuba are people from several black African tribes, and have distinct languages and culture which clashed with the government's Arabist policies and conservative brand of political Islam. ;
Khartoum responded by arming Arab-majority militias.
In 1992, the governor of Southern Kordofan formally declared a jihad – or holy war - in the Nuba Mountains. According to Foreign Policy, the campaign included the use of chemical weapons against the civilian population, starvation, murder, rape, enslavement and land seizure.
Hundreds of thousands of Nuba were forcibly displaced, and as many as 200,000 people died. The north's forces targeted Muslims, as well as Christians and animists.
Unlike Abyei, the 2005 peace deal that ended the civil war did not give the people of Southern Kordofan the right to choose whether to join the north or south.
Many Nuba are demanding political reform and autonomy and thousands still serve in a rebel armed force, the Sudan People's Liberation Movement-North (SPLM-N). The SPLM was a major rebel group during the north-south civil war, and is now the ruling party in South Sudan. It denies supporting SPLM-N rebels across the border.
Tensions in Southern Kordofan rose following the state's May 2011 governorship elections, with SPLM-N saying it had been cheated of victory. Sudan's ruling National Congress Party candidate Ahmed Haroun - who is wanted by the International Criminal Court for alleged war crimes in Darfur - was declared winner and soon afterwards former SPLM fighters were ordered to disarm.
In early June 2011, fighting broke out in the state capital, Kadugli, between SPLM rebels and the northern army supported by Khartoum-backed militias. The SPLM in rural Nuba Mountains quickly consolidated control over its areas, according to Small Arms Survey.
"We are facing the nightmare of genocide of our people in a final attempt to erase our culture and society from the face of the earth," the Episcopal Bishop of Kadugli and the Nuba Mountains Andudu Adam el-Nail, said.
Khartoum accused the rebels of launching an uprising to try and seize control of the state ahead of South Sudan's July 9, 2011 secession.
Hundreds of thousands of civilians have been forced to flee aerial bombardment and ground attacks, according to U.N. reports. Many have sought refuge in South Sudan.
In all, more than one million civilians have been affected by the fighting, the United Nations said in its 2011 third quarter report.
Activists say Sudan government troops and Khartoum-backed Arab militias have targeted Nuba civilians, carrying out bombing campaigns and going house to house killing people. Khartoum has denied the allegations.
Aid agencies are concerned about rising levels of hunger. The fighting has prevented farmers from planting crops in many parts of the state, and it is difficult to transport food or reach markets.
Insecurity and government restrictions have put many of the displaced out of reach of aid, especially those in SPLM-N areas. U.S. officials said government restrictions on U.N. agencies could lead to large-scale famine.
Some experts say Sudan could use famine to flood South Sudan with refugees and destabilise it. Khartoum denies the theory.
In November, the U.S. government condemned the "indiscriminate aerial bombings of civilian targets" by Sudan government forces.
There have also been unconfirmed reports of Sudan bombing refugee camps in South Sudan where many have sought shelter.
Negotiations to resolve the fighting have so far failed, despite mediation by the African Union led by former South African President Thabo Mbeki and then Ethiopia's President Meles Zenawi.
In September 2011, fighting between SPLM-N and Khartoum forces in South Kordofan spread to Blue Nile state.
Sudan's President Omar Hassan al-Bashir immediately called a state of emergency in Blue Nile, sacked state governor Malik Agar of the SPLM-N, and closed SPLM-N's headquarters in Khartoum.
Sudan has complained to the U.N. Security Council, accusing South Sudan of supplying rebels in both Blue Nile and Southern Kordofan with arms. Juba denies the charges.
As with South Kordofan, the government has restricted aid agencies' access to people in need in Blue Nile. The United States and United Nations pressed Khartoum to allow more aid into the state, saying hunger levels were reaching crisis levels.
Tens of thousands have been displaced, and many have fled to South Sudan and Ethiopia.
Under the 2005 peace deal, Khartoum was required to downsize its forces to prewar levels in Blue Nile. But governor Agar said more than 20,000 troops were still stationed there at the end of 2010 on the eve of South Sudan's referendum. The Small Arms Survey says there were also large, but unverifiable, numbers of Popular Defence Forces – a pro-Khartoum militia. Towards the end of 2010, SPLM forces moved into the area.
People in Blue Nile were not granted a referendum to choose whether to join north or South Sudan under the 2005 peace deal. Many who sided with the southern rebels in the civil war felt betrayed.
The peace deal did however call for popular consultations on the state's status, to be held in January 2011. But the consultations stalled after the National Assembly decided in July to extend the process by six months, giving the president the option to extend it further. Governor Agar called the decision a violation of the peace deal and refused to recognise it.
Why is Sudan plagued by internal conflict, and how are these conflicts related, if at all? There is no easy answer, but a few explanations do shed light on the problem.
First, colonisers drew the boundaries of pre-2011 Sudan without heed to the different religious and ethnic groups that already inhabited the territory, which was under joint Anglo-Egyptian control until 1956.
This set the stage for showdowns between the north, populated predominantly by Arab Muslims, and the south, populated largely by animists and Christians of African origin.
The British lit the tinderbox when they left by leaving an elite group of northerners in charge.
Second, over the years those in power in Khartoum marginalised southerners, Darfuris and several other groups in various pockets of the country, including provinces in eastern Sudan. In addition, the Islamist policies of the government in the 1990s added to the alienation of the southerners.
Third, rebels in all corners of the country shared similar grievances over Khartoum's failure to provide even the most basic of services, and widespread abject poverty fuelled calls to share the wealth.
The discovery of oil in southern Sudan in 1978 only raised the stakes. Sudan rakes in billions of dollars a year in oil exports but there is little in the way of social services to show for it.