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Background Twice weekly lateral flow tests (LFTs) for secondary school children was UK Government policy from 8 March 2021. We evaluate use of LFTs (both supervised at test centres, and home test kits) in school-aged children in Cheshire and Merseyside. Methods We report (i) number of LFT positives (ii) proportion of LFT positive with confirmatory reverse transcription polymerase chain reaction (PCR) test within 2 days, and (iii) agreement between LFT-positive and confirmatory PCR, and dependence of (i–iii) on COVID-19 prevalence. Findings 1 248 468 LFTs were taken by 211 255 12–18 years old, and 163 914 by 52 116 5–11 years old between 6 November 2020 and 31 July 2021. Five thousand three hundred and fourteen (2.5%) 12–18 years old and 1996 (3.8%) 5–11 years old returned LFT positives, with 3829 (72.1%) and 1535 (76.9%) confirmatory PCRs, and 3357 (87.7%) and 1383 (90.1%) confirmatory PCR-positives, respectively. Monthly proportions of LFT positive with PCR negative varied between 4.7% and 35.3% in 12–18 years old (corresponding proportion of all tests positive: 9.7% and 0.3%). Deprivation and non-White ethnicity were associated with reduced uptake of confirmatory PCR. Interpretation Substantial inequalities in confirmatory testing need more attention to avoid further disadvantage through education loss. When prevalence is low additional measures, including confirmatory testing, are needed. Local Directors of Public Health taking more control over schools testing may be needed. Funding DHSC, MRC, NIHR, EPSRC. [ABSTRACT FROM AUTHOR]