This study presents results of histopathologic, cytogenetics and flow cytometry analyses performed on Macoma balthica collected from the Gulf of Gdansk (Baltic Sea) in 2003 in order to compare the techniques for diagnosis of neoplasia. The proportion of affected clams gave a crude prevalence of 15.7 %. The four stages of the disease defined by histology and three stages of neoplasia defined by flow cytometry were reported. Stage I defined by flow cytometry corresponded to stages I and II defined by histology. Chromosome analysis did not lead to a staging of neoplastic progression. Both cytogenetics and flow cytometry indicated a difference in the DNA content of non-neoplastic and neoplastic cells. Cytogenetics examination marked that the range of chromosome numbers scored in abnormal mitosis corresponded to pentaploid-like cells (2.37 x diploid) and was similar to the mean DNA quantity identified using flow cytometry (2.36 x diploid). These methods generally have lower diagnosis sensitivity because with both techniques only a part of an animal can be studied. Thus, histology examination appeared to be the most sensitive tool for detection of the possible foci of neoplastic cells, metastasis and rare tumour cells freely circulating in the hemolymph in the early stages of the disease. Cytogenetic analysis has been considered as an important tool for the evaluation of aquatic environment quality as well as for the ecological risk assessment. Flow cytometry provided a rapid and easy method for discrimination of the aneuploid cells within thousands of cells per individual. Thus, in diagnosis of early stages of the cancer as well as early metastasis histology analyses should be performed. Chromosomes analysis and flow cytometry examination are important techniques for detection abnormalities in cell division, cell viability and DNA quantity. They appear to be very important in diagnosis of tumors based on high aneuploidy level.