<jats:title>Abstract</jats:title><jats:p>Introduction – <jats:italic>Melia azedarach</jats:italic> adapted to cool climates was selected as rootstocks for vegetative propagation of <jats:italic>Azadirachta indica</jats:italic>. Cleft grafting of <jats:italic>A. indica</jats:italic> on <jats:italic>M. azedarach</jats:italic> rootstock showed excellent survival. Little is known about the chemistry of grafting.<jats:p>Objective – The roots, stems, leaves and seeds of this graft were examined in order to verify if grafted <jats:italic>A. indica</jats:italic> would produce limonoids different from those found in non‐grafted plants. Intact matured fruits were also studied to verify if they were free of meliatoxins.<jats:p>Methodology – After successive chromatographic separations the extracts afforded several limonoids. HPLC‐MS/MS and MALDI‐MS were used to develop sensitive methods for detecting azadirachtin on all aerial parts of this graft and meliatoxins in fruits, respectively.<jats:p>Results – The stem afforded the limonoid salannin, which was previously found in the oil seeds of <jats:italic>A. indica</jats:italic>. Salannin is also found in the root bark of <jats:italic>M. azedarach</jats:italic>. Thus, the finding of salannin in this study suggests that it could have been translocated from the <jats:italic>M. azedarach</jats:italic> rootstock to the <jats:italic>A. indica</jats:italic> graft. HPLC‐MS/MS analyses showed that azadirachtin was present in all parts of the fruits, stem, flowers and root, but absent in the leaves. The results of MALDI‐MS analyses confirmed the absence of meliatoxins in graft fruits.<jats:p>Conclusion – This study showed that <jats:italic>A. indica</jats:italic> grafted onto <jats:italic>M. azedarach</jats:italic> rootstock produces azadirachtin, and also that its fruits are free of meliatoxins from rootstocks, confirming that this graft forms an excellent basis for breeding vigorous Neem trees in cooler regions. Copyright © 2010 John Wiley & Sons, Ltd.