Bacterial infection is a major cause of morbidity and mortality among patients with HIV living in Africa. Broadening the scope of cotrimoxazole (CTX) prophylaxis to cover patients whose CD4 counts are above 200 cells/mm3 has been suggested as a means of improving the control of infectous disease on the continent. CTX has demonstrated antimalarial benefit in Central and West Africa, but in areas of high bacterial resistance to CTX, the prophylactic role of CTX as an antibacterial agent is less clear. In particular there is little to suggest that prophylactic CTX provides reliable control against the pneumococcus. In both South Africa and the Gambia, several clinical studies with pneumococcal conjugate vaccines have resulted in improved clinical outcomes for children with and without HIV infection. There is clearly much more that needs to be done, and conjugate vaccines provide a unique opportunity to improve the future lives of Africa’s children