Physical activity questionnaires (PAQs) could be suitable tools in free-living people for measures of physical activity, total and activity energy expenditure (TEE and AEE). This meta-analysis was performed to determine valid PAQs for estimating TEE and AEE using doubly labeled water (DLW). We identified data from relevant studies by searching Google Scholar, PubMed and Scopus databases. This revealed 38 studies that had validated PAQs with DLW, and reported the mean differences between PAQs and DLW measures of TEE (TEEDLW -TEEPAQ) and AEE (AEEDLW -AEEPAQ). We assessed 78 PAQs consisting of 59 PAQs that assessed TEE and 35 PAQs that examined AEE. There was no significant difference between TEEPAQs and TEEDLW with a weighted mean difference of -243.3 and a range of -841.4 to 354.6 kJ/day, and a significant weighted mean difference of AEEDLW - AEE PAQs 414.6 and a range of 78.7 to 750.5. To determine whether any PAQ was a valid tool for estimating TEE and AEE, we carried out a subgroup analysis by type of PAQ. Only Active-Q, administered in two seasons, and Three-day PA diaries were correlated with TEE by DLW at the population level, however, these two PAQs did not demostrate an acceptable limit of agreement at individual level. For AEE, no PAQ was correlated with DLW either at the population or at the individual levels. Active-Q and Three-day PA diaries were identified as the only valid PAQs for TEE estimation. Further well designed studies are needed to verify this result and identify additional valid PAQs.