Determine the population prevalence and trends of cleft lip and/or palate (CL/P) by department for Colombia in the period 2009 to 2015. Prevalence study based on Individual Registry of Health Services in general population from 2009 to 2015. All people diagnosed with CL/P were included for all ages, type of diagnosis, and any type of health services in the mentioned period. The prevalence was calculated by period and point for each year, for each department and according to the type of cleft. Stationarity on time series was evaluated using (Dickey-Fuller) and (Phillips-Perron). A trend test was applied to estimate whether the increase in prevalence was significant in the period. The trend test used was a Poisson regression. A total 15 225 people with CL/P were identified, where 53.3% were men. The national period prevalence of CL/P is 3.37 per 10 000 with upward trend (prevalence ratio = 1.34, P = .05) and nonstationary behavior. The national period prevalence of cleft lip is 0.93 per 10 000, cleft palate 1.17 per 10 000, and cleft lip and palate (CLP) 1.26 per 10 000, where CLP is subclassify into unilateral CLP (0.83 per 10 000) and bilateral CLP (0.43 per 10 000). At the departmental level, the highest CL/P prevalence is Guaviare (11.2), followed by Guainía (8.4) and the lowest Quindío (0.49). In Colombia, the national period prevalence of CL/P is 3.37 per 10 000 with upward trend at national level indicates an increase in prevalence from 2009 to 2015. The 77% of the total CL/P population are infant or adolescent. Geographically, the central region has the highest availability of technologies.