A new stimulated echo based pulsed gradient spin–echo sequence, MAG-PGSTE, has been developed for the determination of self-diffusion in magnetically inhomogeneous samples. The sequence was tested on two glass bead samples (i.e., 212–300 and <106 μm glass bead packs). The MAG-PGSTE sequence was compared to the MAGSTE (or MPFG) (P.Z. Sun, J.G. Seland, D. Cory, Background gradient suppression in pulsed gradient stimulated echo measurements, J. Magn. Reson. 161 (2003) 168–173; P.Z. Sun, S.A. Smith, J. Zhou, Analysis of the magic asymmetric gradient stimulated echo sequence with shaped gradients, J. Magn. Reson. 171 (2004) 324–329; P.Z. Sun, Improved diffusion measurement in heterogeneous systems using the magic asymmetric gradient stimulated echo (MAGSTE) technique, J. Magn. Reson. 187 (2007) 177–183; P. Galvosas, F. Stallmach, J. Kärger, Background gradient suppression in stimulated echo NMR diffusion studies using magic pulsed field gradient ratios, J. Magn. Reson. 166 (2004) 164–173, P. Galvosas, PFG NMR-Diffusionsuntersuchungen mit ultra-hohen gepulsten magnetischen Feldgradienten an mikroporösen Materialien, Ph.D. Thesis, Universität Leipzig, 2003, P.Z. Sun, Nuclear Magnetic Resonance Microscopy and Diffusion, Ph.D. Thesis, Massachusetts Institute of Technology, 2003) sequence and Cotts 13-interval [R.M. Cotts, M.J.R. Hoch, T. Sun, J.T. Marker, Pulsed field gradient stimulated echo methods for improved NMR diffusion measurements in heterogeneous systems, J. Magn. Reson. 83 (1989) 252–266] sequence using both glass bead samples. The MAG-PGSTE and MAGSTE (or MPFG) sequences outperformed the Cotts 13-interval sequence in the measurement of diffusion coefficients; more interestingly, for the sample with higher background gradients (i.e., the <106 μm glass bead sample), the MAG-PGSTE sequence provided higher signal-to-noise ratios and thus better diffusion measurements than the MAGSTE and Cotts 13-interval sequences. In addition, the MAG-PGSTE sequence provided good characterization of the surface-to-volume ratio for the glass bead samples.