Background Obstructive apnea is a sleep disorder characterized by pauses in breathing during sleep: breathing is interrupted by a physical block to airflow despite effort. The purpose of this study was to test if osteopathy could influence the incidence of obstructive apnea during sleep in infants. Methods Thirty-four healthy infants (age: 1.5–4.0 months) were recruited and randomized in two groups; six infants dropped out. The osteopathy treatment group (n = 15 infants) received 2 osteopathic treatments in a period of 2 weeks and a control group (n = 13 infants) received 2 non-specific treatments in the same period of time. The main outcome measure was the change in the number of obstructive apneas measured during an 8-hour polysomnographic recording before and after the two treatment sessions. Results The results of the second polysomnographic recordings showed a significant decrease in the number of obstructive apneas in the osteopathy group (p = 0.01, Wilcoxon test), in comparison to the control group showing only a trend suggesting a gradual physiologic decrease of obstructive apneas. However, the difference in the decline of obstructive apneas between the groups after treatment was not significant (p = 0.43). Conclusion Osteopathy may have a positive influence on the incidence of obstructive apneas during sleep in infants with a previous history of obstructive apneas as measured by polysomnography. Additional research in this area appears warranted.