Bronchial hyperreactivity (BHR) is a key feature of asthma, but measurement can usually not be achieved in infants with standard lung function tests. We investigated the safety and tolerability of methacholine challenge in infants with recurrent wheezing episodes. 78 methacholine challenges in 51 sedated infants aged 12-36 months with recurrent wheezing episodes were performed. Methacholine challenge was stopped when clinical signs (coughing, wheezing, or cyanosis) or a drop of oxygen saturation (SPO2) of at least 5% or a drop of transcutaneous oxygen tension (PtcO2) of at least 0.8 kPa or an increase of resistance (RrsSO), of 50% by single occlusion technique were observed. Prior to methacholine challenge, all children were symptom-free with a mean SPO2 of 97.4% (SD 1.80%). In 48 cases (61.5%), no clinical sign was observed, 17 (21.8%) coughed, and 13 (16.7%) wheezed. A mean reduction of SPO2 of 5.0% (SD 3.89%) for the entire population was observed. In 15 of 78 cases, a decrease of SPO2 <90% occurred. This SPO2 drop was short-lasting and resolved spontaneously or after bronchodilator inhalation. Infants whose SPO2 dropped <90% showed a greater increase of RrsSO compared to infants who did not drop <90% (133% vs. 65% RrsSO increase, p<0.001). Methacholine challenge, using a combination of clinical observation, monitoring of SPO2 and PtcO2, and airway resistance using the single-occlusion technique, is a safe and tolerable tool to measure the BHR in infants with recurrent wheezing episodes.