Using loop-specific DNA clones, we established that the T(X:Y)56 (Hackstein and Hennig 1982) chromosome, formerly thought to be deleted for the Yshort arm and the associated 'nooses' loops is actually an XYS X YL combination. It carries, adjacent to the translocation junction, the complete and uninterrupted set of the two dysfunctional 'nooses' domains. The morphologically altered and functionally defective loops are transcribed at about 50% of the normal rate. Transcripts in one of the two 'nooses' domains are preferentially underrepresented and their distribution in the spermatocyte nucleus is distorted, presumably as a consequence of a spreading effect. No alteration in transcript size or in the correct strand selection, and no variegation of transcription on the single spermatocyte level, were observed. In another translocation T(X:Y)97, in which 'tubular ribbons' were reported to be inactivated (Hess 1970), complete elimination of DNA sequences is observed. A possible mechanism for the position effect inactivation of Y loops in X:Y translocations is discussed briefly.