Embryonal tumours, the most common group of malignant solid tumours in children consist about 12-25% of all brain tumours of childhood. The most frequent types are: medulloblastoma (MB), supratentorial primitive neuroectodermal tumour (sPNET) and atypical teratoid/rhabdoid tumour (AT/RT). The loss of genetic material in embryonal tumours is the most often described abnormality, which may be confirmed by loss of heterozygosity analysis (LOH). This method is used to identifying regions harboring putative suppressor genes. 35 children (18 male and 17 female), aged from one year to 13 years were included in this study. There were 26 MB, six sPNETs and three AT/RTs. DNA isolated from tumour tissues and blood samples (control) was amplified in polymerase chain reaction (PCR) with polymorphic markers. Molecular analyses were performed for 35 primary and 12 recurrent tumours. LOH was found in 21 primary tumours (60%). In 14 cases no alteration for all analysed region was confirmed. LOH was detected most often on chromosomes 17p, 22q and 10q. There was no alterations on chromosomes 1p, 1q and 5q. Progression of the molecular changes occurred in one case of recurrent medulloblastoma. LOH on 10q and 17p was found in both primary and recurrent tumour, while losses on 16p and 16q occurred only in the recurrent tumour. The occurrence of LOH in the particular types of tumours is quite different and not specific. Progression of molecular changes in recurrent tumors is rare event and could be connected with radiotherapy.