Secondary montane forest is created by either natural or artificial disturbances resulting in open canopies. It is an important resource in relation to economic and ecological values, however, it faces over-exploitation. The objective of this study was to compare regeneration, forest structure and species diversity of woody vegetation between disturbed and undisturbed sites of the South-Western (SW) Mau forest reserve in Kenya. A nested research sampling design was used, whereby, plots of 500 by 500 m were demarcated in Itare, Maramara and Ndoinet blocks. In disturbed sites, canopy openings were randomly selected to constitute the sample units. In undisturbed sites, sample plots of 30 by 20 m were randomly nested. Regeneration, forest structure and species diversity were then determined per sample unit. Wilcoxon rank sum test with continuity correction was then used to compare the three parameters in disturbed and undisturbed sites of the forest. A total of 41 gaps were selected (7 large, 11 medium and 23 small gap sizes) in disturbed sites while a total of 19 sub-plots (Itare 5, Maramara 6 and Ndoinet 8 times) were laid in undisturbed sites. There was a significant difference in forest structure between disturbed and undisturbed sites of the forest (P = 0.01, P value adjustment method: BH). The forest was invaded by Piper capensis, Ribes spp. and ferns in disturbed sites which affected the three woody vegetation population parameters. Therefore, enrichment planting was recommended in disturbed sites to conserve biodiversity within the forest.