The way infants are fed during the complementary period can have a significant impact on infants’ health and development. Infant cereals play an important role in complementary feeding in many countries. In spite of well documented benefits of a low sugar and high whole grain diet, commercial infant cereals are often refined and contain a high amount of sugars. The aim of the present study was to compare the sensory acceptability, gastrointestinal tolerance and bowel habits of two commercially available infant cereals in Spain with varying sugar and whole grain contents in infants at weaning. Forty-six healthy infants (mean age = 5.2 ± 0.4 months) received one of the two infant cereals containing either 0% whole grain flour and a high sugar content produced by starch hydrolysis (24 g/100 g) (Cereal A) or 50% whole grain flour and a medium-sugar content produced by hydrolysis (12 g/100 g) (Cereal B) in a randomized, triple blind, cross-over controlled trial. Both types of infant cereals were consumed for seven weeks. The cross-over was carried out after seven weeks. Sensory acceptability, anthropometry, gastrointestinal tolerance and adverse events were measured, and results evaluated using a linear regression model. No significant differences were observed between groups in any of the main variables analyzed. Importantly, the long-term health implications of our findings represent a wake-up call for the food industry to reduce or even eliminate simple sugars in infant cereals and for regulatory bodies and professional organizations to recommend whole grain infant cereals.