Since 1986 two West African countries, Benin and Guinea, have been actively reorganizing their peripheral health systems according to strategies subsequently called the "Bamako Initiative". Two preceding articles described the strategies implemented and the increased effectiveness of primary health care (PHC) witnessed over a period of six years. This article presents an analysis of cost and coverage data from biannual monitoring sessions between 1988 and 1993 in approximately 200 health centres in Benin and 214 in Guinea. In order to assess affordability, the total and per capita recurrent costs for operational health centres are analysed and then compared. The cost analysis reveals a mean total cost per health centre per year of slightly over US+11,000 in Benin and nearly US+9,000 in Guinea. The median cost per capita per year is approximately US+1.0 in Benin and between US+0.60 and US+0.80 in Guinea. Comparisons of these costs between regions, health centres and over time (as coverage levels evolved) show very little variation in either country. Cost-effectiveness is estimated by allocating these costs to immunization, antenatal and curative care and comparing them to the coverage achieved with these interventions. First, the cost-effectiveness of the Bamako Initiative (BI) system as a whole is analysed. The cost per fully vaccinated child is calculated at US+10.9 in Benin and US+8.8 in Guinea. The cost per woman receiving at least three antenatal visits is US+7 in Benin and US+4.7 in Guinea. For curative care, cost per full treatment is US+1.6 in Benin and half this amount in Guinea. Cost-effectiveness is variable between regions, health centres reveals that these differences in cost-effectiveness are mainly caused by the coverage levels achieved, since total costs are relatively stable. Finally the efficiency of drug management and prescriptions as well as of outreach for the expanded programme of immunizations (EPI) is estimated by relating specific drug and outreach activities costs to the number of beneficiaries. The average cost of drugs per treatment is around US+0.5 in Benin and around US+0.3 in Guinea. Cost analysis of outreach activities undertaken for EPI in Guinea revealed a similar average cost per child completely vaccinated for health centres with different intensities of outreach (approximately US+10) and an additional cost per child vaccinated attributable to outreach of US+1-2.