Background: The existing literature has conflicting findings about the literacy outcome of children with speech sound disorders (SSD), which may be due to the heterogeneity within SSD. Previous studies have documented that two important dimensions of heterogeneity are the presence of a comorbid language impairment (LI) and the persistence of SSD, but these factors have not been examined separately. Method: The current study used a 2 x 2 MANOVA design (with follow-up MANCOVAs) to examine how a comorbid language impairment (LI) and the persistence of SSD relate to pre-literacy skills in a sample of 5- to 6-year-old children with SSD. Results: Significant main effects for persistent SSD and LI were obtained, such that each factor was associated with worse performance on pre-literacy tasks, particularly those assessing phonological awareness (even with nonverbal IQ covaried). In addition, even SSD children with normalized speech without LI were found to have deficits on phonological awareness tasks relative to control participants. Conclusions: These results suggest that a history of SSD and comorbid LI are strong correlates of pre-literacy deficits.