Floral scent plays an important role in attracting and guiding pollinators and is composed of a bouquet of volatile organic compounds (VOCs). Alstroemeria is a commercially important cut flower, however breeding efforts have focussed on flower colour and size rather than scent. Recently analysis of two scented cultivars derived from the scented Alstroemeria caryophyllaea revealed a surprising divergence in VOC profiles. Here 13 scented lines of A. caryophyllaea derived from selfing were characterized including morphology, evaluation of the floral scent through GC–MS and sensorial analysis. Leaf shape, stem length, flower size, shape, colouration and productivity all varied between lines. Sensorial analyses indicated that two lines (C013 and C017) were most highly rated for their appearance and C017 was also scored highest for its scent contrasting with C004 which scored lowest. Analyses of scent bouquets from six of the lines revealed 23 terpenoid compounds. All lines showed the same most abundant compound putatively identified as β-trans-ocimene, and three further compounds were discriminatory amongst the lines following PCA. Genomic organization of AlstroTPS, a previously identified myrcene synthase, showed substantial polymorphism between lines. The multifactorial characterization performed in this study showed differences among the lines confirming parental heterozygosity.