Habaj is the author of the monographs Druhá moderna (The Second Modernism, 2005), Model človeka a sveta v básnickom diele Jána Smreka (A Model of a Person and the World in the Poetry of Ján Smrek, 2013), and Básnik v čase. Smrek – Lukáč – Novomeský – Poničan (A Poet in Time, 2016). He edited the anthology Druhá moderna. Slovenská modernistická próza (The Second Modernism. Slovak Modernist Prose, 1918) and co-wrote and co-edited the collective scientific monography Modernizmus v pohybe (Modernism in Motion, 2019).
He has written the following collections of poetry: 80-967760-4-5 (1997); Gymnazistky. Prázdniny trinásťročnej (Grammar School Girls. A Thirteen-Year-Old’s Holidays, 1999); Korene neba. Básne z posledného storočia (The Roots of Heaven. Poems from the Last Century, 2000); Básne pre mŕtve dievčatá (Poems for Dead Girls, 2004); Michal Habaj (2012, 2nd edition in 2018) and Caput Mortuum (2015, 2nd edition in 2017). Using the pen-name, Anna Snegina, he has published two collections of poems titled Pas de deux (2003) and Básne z pozostalosti (Poems from the Remains, 2009). He is one of the co-authors of the experimental poetry projects Generátor X: Hmlovina (Generator X: Mist, 1999) and Generator X_2: Nové kódexy (Generator X_2: New Codes, 2013). He is also co-author of the poetry book The European Constitution in Verse (Brussels, 2009).
His poems have been translated into most European languages and featured in many international anthologies. Books with selected poetry of his came out in Mexico -- Nostalgia o Invierno en Bratislava (2018) -- and in Germany -- Erwachen (2021). His poetry collections Caput Mortuum and Michal Habaj were published in Hungarian translation (2019, 2020).