Cytogenetics of solid tumors has been substantially improved by novel techniques such as interphase fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH), the applications of which are summarized in this review with focus on clinical implications. In breast cancer, and similarly in carcinoma of the lung, pancreas and urinary bladder, FISH is of diagnostic value in diagnostic workup of primary and metastatic tumor material. Amplifications of erbB2, c-myc and 20q13, which are prognostically relevant in breast cancer, were rapidly and sensitively detected by molecular cytogenetics. In head and neck tumors, the phenomenon of field cancerization with accumulating genetic alterations was studied by interphase FISH, which could serve as a tool to identify premalignant lesions at risk of transformation. Prostatic cancer with a more aggressive behavior is significantly associated with changes involving chromosomes 7, 8, X and Y, with a great impact on therapeutic decisions. Isochromosome i(12p), specific for germ cell tumors, is sensitively detected by various novel approaches and may be the only feature characterizing very undifferentiated midline tumors of unknown origin, which are potentially cured with adequate treatment. Finally, the assessment by FISH of ploidy status and of N-myc amplification in neuroblastoma may also be helpful in applying a risk-adapted therapeutic strategy.