The influence of visuo-spatial skills on numerical magnitude processing is the subject of a long-standing debate. As most of the numerical and non-numerical magnitude abilities underpinning mathematical development are visual by nature, they are often assessed in the visual modality, thereby confusing visuo-spatial and numerical processing. In order to assess the influence of visuo-spatial processing on numerical magnitude representation, we examined magnitude processing in patients with 22q11.2 deletion syndrome (22q11DS), a genetic condition characterized by a cognitive profile with a relative weakness in visuo-spatial abilities but with preserved verbal abilities. Twenty-seven participants with 22q11DS were compared to two control groups (one matched on verbal intelligence and the other on visuo-spatial abilities) on several magnitude comparison tasks each with different visuo-spatial processing requirements. Our results showed that participants with 22q11DS present a consistent pattern of impairment in magnitude comparison tasks requiring the processing of visuo-spatial dimensions: comparison of lengths and collections. In contrast, their performance did not differ from the control groups in a visual task with no spatial processing requirement (i.e. numerical comparison of flashed dot sequences) or in auditory tasks (i.e., duration comparison and numerical comparison of sound sequences). Finally, a specific deficit of enumeration processes was observed in the subitizing range. Taken together, these results show that deficits in magnitude can occur as a consequence of a visuo-spatial deficit. This highlights the influence of the nature of the tasks selected to assess magnitude representation.