Screening for 22q11.2 deletions has not an easy approach due to the wide variability of their associated phenotype. Many clinical features overlap with those of other known syndromes and reported loci. Patients referred to exclude a 22q11.2 deletion are usually tested with a locus-specific FISH probe, with 10% positive cases depending on the selection criteria, but patients testing negative for FISH at 22q11.2 may have other chromosomal aberrations in routine cytogenetic analysis. We tested 819 patients suspected of having a 22q11.2 deletion. Eighty-eight patients (10.7%) were positive for 22q11.2 deletion, whereas 30 patients (3.7%) showed other chromosomal abnormalities involving deletions and duplications, derivative chromosomes, marker chromosomes, apparently balanced and unbalanced translocations and sex chromosome aneuploidies. Of these alterations, 28 did not involve region 22q11 and most had not been associated with 22q11.2 deletion phenotype before. We discuss the similarity of DiGeorge/velocardiofacial syndrome with other known clinical entities and suggest correlations between the new loci and the observed clinical features. The frequency of unrelated chromosomal anomalies reported in this study and in other previous reports highlights the importance of conventional cytogenetic analysis as an initial genome-wide screening tool in all referred patients, and provides useful data to optimize diagnostic and screening protocols according to the most frequent chromosomal findings.