The NLMS is based on specific survey months of the Current Population Survey, the Annual Social and Economic Supplement, and a subset of the 1980 Census. These are one-time data collection processes with no subsequent data collection follow up. Therefore, one limitation of NLMS data is that they provide a one-time only, baseline, measurement of subjects in a long-term follow-up situation. Another limitation of these data is that, although the CPS and census instruments do provide extensive data collection capabilities in specific subject matter areas, desirable general or specific health information is not collected, and smoking status is available on only a limited number of records.

The assurance of confidentiality of Census Bureau data is provided by Title 13 of the United States Code (U.S.C.). As such, NLMS operational procedures carefully follow the well-defined practices designed to maintain the confidentiality of personal records as required by Title 13. These practices include the prevention of disclosure through the elimination of sparse cells in publications, the prohibited release of small-area geographical information on the NLMS public-use files, the use of an individually assigned NLMS control number to identify records instead of the use of personal identifiers for these purposes, and the restriction of persons having direct access to the NLMS database. A violation of Title 13 restrictions includes loss of job and assessment of severe penalties including a prison term of up to 5 years and/or fines of up to $500,000, for any individual found guilty of releasing confidential information. In addition, any data acquired from an external agency for NLMS purposes is acquired under the same strict confidentiality protections and practices of Title 13.