Congenital malformations and cancer may share common etiological factors and the association between nonsyndromic cleft lip and/or palate (NSCL/P) and cancers has been observed in different studies. The objective of this study was to evaluate the frequency of cancer in relatives of patients with NSCL/P. This investigation was a cross-sectional, case-controlled study, evaluating 358 patients with NSCL/P treated at a Referral Center for craniofacial deformities (case group) and 358 patients without craniofacial alterations (control group). Information concerning the gender, age and family history of cancer in first-degree relatives for both groups was obtained. The frequency of cancer was 6.4% (n=46) in the studied population, with 18 subjects in the case group (5%) and 28 (7.8%) in control. In both groups, the most frequently reported cases were those of breast, colorectal, stomach, prostate and uterus cancers, but there was no association between the two groups. There was no association with a family history of cancer among the first-degree relatives (odds ratio=0.62; 95% IC: 0.34 to 1.15), neither when the analysis was made by type of cancer. In conclusion, both epidemiological and genetic studies have suggested common etiological factors for NSCL/P and cancer. However, in this population-based study, no association between cancer and NSCL/P could be confirmed.