Objectives Research increasingly indicates the importance of the nutritional programming that occurs in the first 2– 3 years of life. Quality nutrition during this brief window has been shown to have large and significant effects on health and development throughout childhood and even into adulthood. Despite the widespread understanding of this critical window, and the long-term consequences of leaving nutritional deficiencies unaddressed, little is known about the status of infant nutrition in rural China, or about the relationship between infant nutrition and cognitive development in rural China. Design, setting and participants In April 2013 and October 2013, we conducted a survey of 1808 infants aged 6– 12 months living in 351 villages across 174 townships in nationally designated poverty counties in rural areas of southern Shaanxi Province, China. Main outcome measures Infants were administered a finger prick blood test for haemoglobin and assessed according to the Bayley Scales of Infant Development. They were also measured for length and weight. Caregivers were administered a survey of demographic characteristics and feeding practices. Results We found that 48.8% of sample infants were anaemic, 3.7% were stunted, 1.2% were underweight and 1.6% were wasted. Approximately 20.0% of the sample infants were significantly delayed in their cognitive development, while just over 32.3% of the sample infants were significantly delayed in their psychomotor development. After controlling for potential confounders, infants with lower haemoglobin counts were significantly more likely to be delayed in both their cognitive (p$<$0.01) and psychomotor development (p$<$0.01). Conclusions The anaemia rates that we identify in this study classify anaemia as a `severe' public health problem according to the WHO. In contrast, there is virtually no linear growth failure among this population. We find that low haemoglobin levels among our sample population are associated with significant cognitive and psychomotor delays that could eventually affect children’s schooling performance and labour force outcomes. Trial registration number ISRCTN44149146.