In order to establish a direct and high performance detection system for cell counts in leaves of Arabidopsis thaliana, wild type (Col) and replication factor C subunit 3 mutant (rfc3–1) plants were selected as materials to study the effects of gene mutation on cell counts by the approach of flow cytometry after enzyme digestion, cell lysis, nuclear collection and dyeing. The results showed that cell counts in the first and the second or the 3rd and the 4th of true leaf in wild type plants were 1.6 or 2.6 times that of rfc3-1 mutant plants respectively. It was indicated that proliferation of leaves was severely affected by gene mutation of RFC3.The established detection system for cell counts of leaves in Arabidopsis was direct and efficient with coefficient of variation (cv) less than 5%.