Cognitive skill differences that are apparent early in pre-kindergarten (pre-K) might provide predictive insights into risk for learning difficulties at school entry, particularly around early markers of risk for comorbid difficulties in early math and literacy. Domain-specific abilities (approximate number system or ANS acuity, phonological awareness) and domain-general abilities (working memory, vigilance, executive attention, and nonverbal IQ) were assessed in 493 children at the beginning of pre-K, to better understand how each uniquely contributes to risk for math difficulties (MD), and comorbid math and reading difficulties (MDRD). At the end of pre-K, standardized math and reading tests were used to form three risk groups (MD, MDRD, not-at-risk) with two severity cut points for math and reading (=25th, =16th percentiles). Discriminant function analysis was used to determine whether and in what ways the groups differed on the cognitive variables. Both MD and MDRD-risk groups differentiated from the not-at-risk group on all variables except for ANS acuity, a finding that was convergent across severity cut points. The only significant contrast for ANS acuity emerged between the most severe MD only group and the not-at-risk group. Only vigilance or sustained attention supported the differentiation of MD risk from MDRD risk. Consistent with school-age studies of comorbidity, MDRD risk was also associated with the lowest levels of math and cognitive skills in this pre-kindergarten sample. Results reveal a potential specific role for sustained attention as an early risk factor for comorbid MDRD, a severe form of learning disability.