Shakespeare’s opposition towards some aspects of Stoic and Neoplatonic doctrines and religious fanaticism, particularly Puritanism, can be found in many of his plays. However, rather than focusing on the dramatic output, this essay will concentrate on Shakespeare’s Sonnets. The strongly subversive nature of the Dark Lady section is especially notable, although modern critical opinion is generally less inclined to acknowledge its subversive philosophical message because of the supposedly more ‘personal’ nature of lyrical expression compared to the dramatic. In fact, critics have generally chosen to focus their attention on the Fair Youth section, more or less intentionally ignoring the Sonnets’ second part, summarily dismissed as an example of parodic inversion of the Petrarchan model, thus avoiding an examination of its profound revolutionary character, that is – an implicit rejection of the Christian and Neo-platonic basis of the sonnet tradition. Through a close reading of two highly meaningful sonnets, this essay will show that, in the poems dedicated to the Dark Lady, Shakespeare calls into question, through clear terminological reference, the very foundations of Christian and Neo-platonic thought – such as the dichotomous nature of creation, the supremacy of the soul over the body, the conception of sin et cetera – in order to show their internal inconsistencies, and to propose instead a new ontological paradigm, based on materialistic and Epicurean principles, that proclaims reality to consist of an indissoluble union of spirit and matter. This secular outlook, whilst not atheistic in the contemporary sense of the term, reveals the deep modernity of Shakespeare’s position, whilst also highlighting the difficulty that some readers still have with bard’s most ‘heretical’ side.