Objective To investigate the incidence of candidal colonization and to analyze its risk factors in patients with connective tissue diseases (CTDs). Methods Throat swabs, midstream urine and anal swabs from 153 patients with CTDs and 63 healthy volunteers were collected for fungus culture. The logistic regression was completed via the software package SPSS 11.0. Results The incidence rate of candidal colonization was higher in the patients than that in the healthy controls (35.29% vs 7.59%). Of all the isolated fungus strains, the proportion of Candida albicans was the highest. The logistic regression analysis revealed that decrease of blood erythrocytes, increase of urine protein, decrease of complements such as CH50, C3 and C4 in serum, high daily dosage of corticosteroids and broad-spectrum antibiotic administration all significantly increased the risk of candidal colonization (all P 0.05). Conclusions The incidence rate of candidal colonization in patients with CTDs is higher than that in healthy controls. Avoiding the risk factors will help to decrease the incidence of candidal colonization in CTDs.