To establish a laboratory iodization quality assurance system to support small-scale salt production facilities in India and to assess the level of agreement for the internal quality assurance (IQA) and external quality assurance (EQA) protocols.

Operational research. The IQA and EQA programme was established in the year 2008. Agreement between field laboratories and the reference laboratory for estimation of iodine content of salt from 2008 to 2011 was assessed. Agreement was assessed using the χ2 test, kappa statistics and the Bland–Altman plot.

Small-scale salt producers in the states of Andhra Pradesh, Gujarat, Rajasthan, Tamil Nadu, Odisha and Karnataka; ‘field laboratories’ supporting the small-scale salt producers; and the ‘reference laboratory’ of the Regional Office (South Asia) of the International Council for the Control of Iodine Deficiency Disorders.

Three hundred small-scale salt producers in the states of Andhra Pradesh, Gujarat, Rajasthan, Tamil Nadu, Odisha and Karnataka and seventeen ‘field laboratories’.

A total of 6573 salt samples for IQA and 347 salt samples for EQA were exchanged between field and reference laboratories during 2008–2012. Out of the total salt sample exchanges, 527 were from Andhra Pradesh and Odisha, 2343 from Gujarat, 2016 from Rajasthan and 1677 from Tamil Nadu and Karnataka. The overall between-laboratory agreement was for 61·6 % for IQA and 64·8 % for EQA. The mean difference between iodine content estimation of field laboratories and the reference laboratory was 0·3 ppm (sd 8·2 ppm) for IQA and –0·3 ppm (sd 3·5 ppm) for EQA.

Our study successfully documents implementation of a laboratory iodization quality assurance protocol in laboratories supporting small-scale salt production facilities in India.