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Puerto Rico has the highest asthma prevalence in the US. In the states, mold exposures have been linked to the development and exacerbation of asthma. For a pilot study of mold populations in Puerto Rico, dust and air samples were collected in January 2013 inside and outside of residences (n = 10) in the north eastern quadrant of Puerto Rico. Inside and outside (protected from rain) settled dust was collected by wiping above floor or ground-level surfaces with a Swiffer (TM) duster cloth. Air samples were collected in five of the residences inside and five matching outside onto Malt Extract Agar and also onto G25N Agar. The dust (5 mg) was analyzed using mold-specific quantitative PCR and mold contamination estimated using the Environmental Relative Moldiness Index (ERMI) metric. Air sampled (150 l) plates were incubated and resulting mold colonies enumerated. The ERMI values were significantly (p = 0.03) greater inside the homes than outside, 20.37 versus 12.55, respectively. Aspergillus penicillioides, A. sydowii, Chaetomium globosum, the Eurotium group and Penicillium crustosum and A. ustus were found in significantly greater numbers inside than outside Puerto Rican residences based on the Wilcoxon rank sum test. However, after correction for multiple comparisons using the Holms-Bonferroni test, only the Eurotium group remained significantly greater. Air samples suggested higher culturable concentrations of molds outside but the differences were not significantly different. Although this is a small study, it suggests that some people in Puerto Rico are exposed to significantly higher mold concentrations indoors than outdoors.