Maize is characterized by high degrees of genomic complexity, genetic diversity, and hybrid vigor.  Variation in small RNAs (sRNAs) influences both genome structure and expression, and thus may contribute to hybrid vigor.  Maize hybrids produce larger and greatnumber er of organs compared to their inbred parents, indicating differences in meristem activity are a key contributor to heterosis. We used Illumina deep sequencing to assess how maize sRNA populations within the seedling shoot apex vary between two maize inbred lines (B73, Mo17) and their reciprocal hybrids that exhibit high heterosis.  Most classes of sRNAs do not differ in relative abundance between the parents or between parents and hybrids, the major exceptions being sRNAs associated with the amplification of post-transcriptional gene silencing.  These sRNAs include non-canonical sRNAs, 21-nucleotide small interfering RNAs (siRNAs) produced from variant alleles at TAS3 loci, and 22-nt siRNA clusters derived from retrotransposons.  Hybridization combines these parental differences in a primarily additive fashion with a trend toward low-parent expression levels, resulting in hybrids that differ from both parents in their complexity of sRNAs and potential for silencing of repetetive sequences.  Loss of the RNA-dependent RNA polymerase (RDR2) encoded by the modifier of paramutation (mop1) locus does not suppress heterosis for B73 x Mo17, which supports our finding that nearly all 24-nt siRNA clusters are found in both inbred parents and do not change upon hybridization.  The observed changes in RNA silencing of repeat sequences are intriguing with respect to the properties of hybrid vigor in maize, as they differ between parents, their effects are distributed throughout the genome, and their potential for amplification could generate non-additive phenotypic effects on meristem activity and growth.