The goal of this study was to identify causes for lower population densities of mouse lemurs (Microcebus murinus) in secondary than in primary dry deciduous forests of western Madagascar. Variations in the abundance of Microcebus murinus are linked to the capacity to enter energy-saving torpor during the dry season. Under natural conditions in primary forest, Microcebus murinus can maintain daily torpor (and possibly hibernation) as long as body temperatures remain below 28°C. Females are more likely to hibernate than males, resulting in skewed sex ratios of captured Microcebus murinus in the primary forest. In the secondary forest the sex ratio of subjects captured during the dry season is more balanced than in primary forest, indicating that fewer females go into torpor in secondary than in primary forest. Secondary forests have fewer large standing or fallen trees that might provide holes as shelter for Microcebus murinus. Ambient temperatures are higher in secondary than in primary forests and higher outside than inside tree holes. These high ambient temperatures might hinder the ability of Microcebus murinus to maintain torpor for prolonged periods in secondary forests. Mouse lemurs from secondary forest have lower body mass than in primary forest. The year-to-year recapture rate is zero in secondary forest and thus significantly lower than in primary forest. This indicates that survival rates are lower in secondary than in primary forests. Thus, secondary forests may be of limited value as buffer zones or even corridors for mouse lemurs.