The prevalence of clusters with the increased morbidity rate is the area of interest among epidemiologists. Not only does the identification of clusters require collecting precise epidemiological data but it also requires the application of reliable spatial statistics techniques. The identification of atypical clusters in this article is performed using data from the Polish Registry of Congenital Malformations (PRWWR) on children with isolated cleft lip with or without cleft palate; the study was carried out in the Wielkopolska Region (Greater Poland). For this purpose, Kulldorff Scan Statistics and the LISA method were used. Since each technique used in the study focuses on a slightly different aspect of spatial structure, the obtained clusters do not always completely overlap. This study presents and compares the efficiency and accuracy of these two non-standard methods of geo-static analysis in children living in the Greater Poland counties. The study has identified 5 agglomerations with an increased prevalence rate of the examined malformation, no statistically significant cluster has been detected. On the basis of the agglomerations, it was possible to compare the applicability of two statistical methods used in the study. Despite the fact that the located clusters do not always completely overlap, the study has proved similarity in qualifying particular counties for given clusters and areas outside the clusters. Taking into account its applicability and monitoring the process of spatial scanning, the Kulldorff method has occurred more universal and accurate in examining the children with congenital malformations.