An efficient system for the analysis of total alkaloids extracted from the aerial parts from different species of genus Haplophyllum (Rutaceae) by HPLC on a reversed-phase column is described. The HPLC method described was validated for its specificity, linearity and precision using external standards (haplopine, skimmianine and haplamine). The chromatographic conditions allowed the separation of alkaloids and the quantification of haplopine, skimmianine and haplamine in different samples of species of Haplophyllum collected in Uzbekistan. The alkaloidal contents of samples were compared with their in vitro cytotoxic properties against two cancer cell lines (HeLa and HCT-116). The cytotoxicity of extracts was correlated with the concentration of haplopine, skimmianine or haplamine in aerial parts of species of Haplophyllum.