In this article, preProgress in Reading Literacy Study (prePIRLS) 2011 data is used to compare the performance of different language of instruction groupings (English, Afrikaans and African languages) in primary schools on the more complex, higher-order reading comprehension items tested in a large-scale international test. PrePIRLS 2011 (N=15,744) was conducted in South Africa's eleven official languages. Schools were sampled according to the language of learning and teaching (LoLT) in Grades 1-3 and the reading comprehension test was administered in that same language. To examine bilingual effects, a sub-sample was drawn from the national dataset that consisted of low socio-economic status (SES) learners whose first language was not English (but who had received instruction in English from grades 1-3) as well as low SES learners who received their Foundation Phase instruction in one of the African languages as a mother tongue. A linear regression (n = 6,342) showed that low socio-economic status (SES) learners whose language of instruction is English, despite it not being their mother tongue, benefitted by 20.35 score points with a t-value of 3.19. This is significant at the 0,01 level (equivalent to half a year) from being in the English L2 group, in comparison to the African languages L1 group, as a measure of achievement on the higher-order subscale. It is argued in this paper that learners whose LoLT is English, but who do not speak English as a home language and tend to be part of the most disadvantaged sector of the population, perform better on the higher-level reading comprehension processes when compared with African language mother tongue instruction across the same grades and socio-economic status. The findings highlight the importance of improved English second language instruction for all LoLT groupings.