The “difference or delay paradigm” focuses on the question of whether children with developmental disabilities (DD) develop in a way that is only delayed, compared to typically developing children, or also qualitatively different. The current study aimed to examine whether qualitative differences exist in cognitive development of young children with and without DD on the basis of item scores on the Dutch Bayley-III Cognition scale. Differential Item Functioning was identified for 15 of the 91 items. The presence of DD was related to a higher number of Guttman errors, hinting at more deviation in the order of skill development. An interaction between group (i.e., with or without DD) and developmental quotient appeared to predict the number of Guttman errors. DD was related to a higher number of Guttman errors for the whole range of developmental quotients; children with DD with a small developmental quotient had the highest number. Combined, the results mean that qualitative differences in development are not to be excluded, especially in cases of severe developmental disabilities. When using the Bayley-III in daily practice, the possibility needs to be taken into account that the instruments’ assumption of a fixed order in skill development does not hold.