We report results of the National External Quality Assessment for (NEQA) laboratories in Burkina Faso, a country with limited resources located in West Africa whose epidemiology is dominated by infectious diseases. The national laboratory network consists of 160 laboratories including 40 private. The Government of Burkina Faso has adopted a national laboratory policy. One of the objectives of this policy is to improve the quality of laboratory results. One of the strategies to achieve this objective is the establishment of a NEQA. The NEQA is a panel testing also called proficiency testing. It is mandatory for all laboratories to participate to the NEQA. The NEQA is organized twice a year and covers all areas of laboratories (bacteriology-virology, biochemistry, hematology, parasitology and immunology). The review of three years of activity (2006-2008) shows the following results: (1) for microscopic examination of bacteria after Gram staining, the error rate decreased from 24.7% in 2006 to 13.1% in 2007 and 13% in 2008; (2) errors rate in reading slides for the microscopic diagnosis of malaria were 23.4%, 14.6% and 10.2% respectively in 2006, 2007 and 2008; (3) for biochemistry, the percentages of unsatisfactory results were respectively 12.5%, 14.8% and 13.8% in 2006, 2007 and 2008 for the overall parameters assessed. The analysis of the results generated by the laboratories during these three years shows a quality improvement. However, the NEQA should be strengthened through ongoing training and quality control of reagents and equipment.