Multiple imputation in business establishment surveys like BRDIS, an annual business survey in which some companies are sampled every year or multiple years, may enhance the estimates of total R&D in addition to helping researchers estimate models with subpopulations of small sample size. Considering a panel of BRDIS companies throughout the years 2008 to 2013 linked to LBD data, this paper uses the conclusions obtained with missing data visualization and other explorations to come up with a strategy to conduct multiple imputation appropriate to address the item nonresponse in R&D expenditures. Because survey design characteristics are behind much of the item and unit nonresponse, multiple imputation of missing data in BRDIS changes the estimates of total R&D significantly and alters the conclusions reached by models of the determinants of R&D investment obtained with complete case analysis.