The Uganda Bureau of Statistics (UBOS), under the mandate of the UBOS Act of 1998, conducts establishment surveys every five to ten years to obtain information on economic activities. The UBI 2009/10 is the most recent establishment survey and was conducted in 2011/121. The UBI 2009/10 findings revealed that the economy is highly informal based given that it had the highest number of establishments (96 percent) and employed the highest number of persons (82 percent). To provide a greater coverage of the informal sector, both the household and nonhousehold based establishments were combined. The household based establishments were covered under the Uganda National Household Survey (UNHS) 2009/10 using the Uganda Population and Housing Census 2002 as the sampling frame. A two-stage stratified sampling design was used to draw the sample. The non-household based establishments were covered under the UBI 2009/10 and the Census of Business Establishments (COBE) 2010/11 was the sampling frame. Stratified sampling design was used to select the sample. Among the major challenges was administering the long questionnaires for large establishments, administering the right questionnaire to the right respondent, locating the establishments, obtaining data from establishments with informal setting, among others. This paper therefore presents data collection challenges in establishment surveys and in particular the UBI 2009/10 experience and in certain instances providing some possible solutions. Highlighting these issues and experience sharing, I believe that this information will be of help in future planning and undertaking such kind of surveys.