Whitebark pine (Pinus albicaulis Engelm.) has recently experienced high mortality due to multiple stressors, and future population viability may rely on natural regeneration. We assessed whitebark pine seedling densities throughout the US Rocky Mountains and identified stand, site, and climatic variables related to seedling presence based on data from 1,217 USDA Forest Service Forest Inventory and Analysis plots. Although mean densities were highest in the whitebark pine forest type, 83% of sites with seedlings present occurred in non-whitebark pine forest types, and the highest densities occurred in the lodgepole pine forest type. To identify factors related to whitebark pine seedling presence, we compared the results generated from three statistical models: logistic regression, classification tree, and random forests. All three models identified cover of grouse whortleberry (Vaccinium scoparium Leiberg ex Coville) as an important predictor, two models distinguished live and dead whitebark pine basal area and elevation, and one model recognized seasonal temperature. None of the models identified forest type as an important predictor. Understanding these factors may help managers identify areas where natural regeneration of whitebark pine is likely to occur, including sites in non-whitebark pine forest types.