Soil from industrial and landfill sites affected by anthropogenic activity was screened for implicit negative effects in an Allium test-system in relation to geochemistry. The concentrations of 15 elements were compared to the ecotoxicologically-based soil guideline values. Admitted geoindices were used to classify test-soils according to risk/hazard categories. Test-soils were screened for the possible deleterious effects in common onion (Allium cepa L.) by employing a test battery of cytogenetic bioassays (root growth inhibition, mitotic activity, frequency of chromosome aberrations and micronuclei, and cell death rate) complemented with two assays of molecular DNA markers, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR). Soil from industrial sites was more severely polluted and more cytotoxic for onions compared to soil from landfill sites. However, the cyto/genotoxic outcome of soil exposure in A. cepa was the same for all test-soils; the detrimental effects were observed in onions treated with every test-soil. Thus, test-soils could not be classified as non- and genotoxic, although certain of them had permissible contamination levels. The chromosome aberration frequency and cell death rates were consistent with the intensity of soil contamination, contrary to the micronuclei rate, which was independent of the soil risk/hazard level. Despite a relationship between risk (RI) and total soil contamination (Z) geoindices, both indices correlated with a different Allium cyto/genotoxicity endpoint, although the Z index was preferred over the RI index as being more informative in correlation analysis. Allium bioassays complemented each other by depicting different aspects of exposure to toxic substances, and determination of cyto/genotoxicity in a battery of different bioassays is important in the risk assessment of ecologically dangerous soils, and an application of a test battery is strongly advised.