Bt cotton was introduced in Burkina Faso (West Africa) in 2008, while countries that adopted Bt cotton earlier have been facing increasing pressure by sucking pests. We conducted a three year comparative study in Bt and non-Bt cotton fields of South-West Burkina Faso to assess hemipteran populations and to detect potential insect outbreaks as observed in other countries such as China and USA. Hemipteran insect sampling was carried out three times per year and insect abundance was evaluated on the base of families. The study was complemented with a three year damage assessment on leaves and bolls and a boll production analysis in 2010. Cicadellidae (Typhlocibinae), Pyrrhocoridae, Pentatomidae, Coreidae and Miridae had the highest incidence in cotton fields. The dominant trend in their population dynamics shows higher insect frequencies in Bt cotton and an increase over time in both cultivars (Bt or non-Bt). Leaf and boll damages were significantly higher in Bt cotton than in non-Bt cotton. Our study suggests different and additive possible causes of the hemipteran outbreak that should further be investigated in depth: 1 - the reduction of insecticide spray numbers in Bt-cotton fields, 2 - the loss of genetically inherited resistance (leaf hairiness), 3 - the decreasing efficacy of insect control programs in non-Bt cotton and (particularly) 4 - the emergence of insecticide resistance in some hemipteran populations, especially in non-Bt fields. The authors also draw the attention of the Burkinabe cotton sector stakeholders on the importance of a quick implementation of IPM measures to guarantee the sustainability of Bt-cotton cultivation in Burkina Faso.